Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer

Luan, Binquan; Afzali, Ali; Harrer, Stefan; Peng, Hongbo; Waggoner, Philip S.; Polonsky, S.; Stolovitzky, Gustavo; Martyna, Glenn

doi:10.1021/jp108865q

Cited by 25 publications

(34 citation statements)

References 31 publications

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“…Interestingly, in the nanochannels seeded with 0.5× TBE, we observed intermittent (stick-slip) motion of the DNA molecules through the nanochannel similar to previous reports 32, 84 at measurements performed <150 V/cm (Figure 6c). Based on MD simulations 96 and theoretical computations, 97 a highly negatively charged DNA molecule translocating through a nanochannel interacts both electrically (attractive or repulsive forces) and hydrodynamically with the channel wall. Therefore, we attributed the intermittent motion of DNA to latent electrical interactions between the charged DNA molecule and the thick EDL and this presents the possibility that at this field strength, the driving force was less than the interfacial force.…”

Section: Resultsmentioning

confidence: 99%

Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels

Uba

Pullagurla

Sirasunthorn

et al. 2015

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107

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Thermoplastics have become attractive alternatives to glass/quartz for microfluidics, but the realization of thermoplastic nanofluidic devices has been slow in spite of the rather simple fabrication techniques that can be used to produce these devices. This slow transition has in part been attributed to insufficient understanding of surface charge effects on the transport properties of single molecules through thermoplastic nanochannels. We report the surface modification of thermoplastic nanochannels and an assessment of the associated surface charge density, zeta potential and electroosmotic flow (EOF). Mixed-scale fluidic networks were fabricated in poly(methylmethacrylate), PMMA. Oxygen plasma was used to generate surface-confined carboxylic acids with devices assembled using low temperature fusion bonding. Amination of the carboxylated surfaces using ethylenediamine (EDA) was accomplished via EDC coupling. XPS and ATR-FTIR revealed the presence of carboxyl and amine groups on the appropriately prepared surfaces. A modified conductance equation for nanochannels was developed to determine their surface conductance and was found to be in good agreement with our experimental results. The measured surface charge density and zeta potential of these devices were lower than glass nanofluidic devices and dependent on the surface modification adopted, as well as the size of the channel. This property, coupled to an apparent increase in fluid viscosity due to nanoconfinement, contributed to the suppression of the EOF in PMMA nanofluidic devices by an order of magnitude compared to the micro-scale devices. Carboxylated PMMA nanochannels were efficient for the transport and elongation of λ-DNA while these same DNA molecules were unable to translocate through aminated nanochannels.

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Section: Resultsmentioning

confidence: 99%

Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels

Uba

Pullagurla

Sirasunthorn

et al. 2015

Analyst

107

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“…This effect was previously observed for DNA translocation studies in nanocolumns 34,45,46 and arose from adsorption/desorption behavior of the solute with the channel walls. 47–49 In addition, this stick/slip motion can arise from dielectrophoretic trapping as well, which results from column wall surface roughness producing inhomogeneity in the electric field. 34 …”

Section: Resultsmentioning

confidence: 99%

Electrophoretic Separation of Single Particles Using Nanoscale Thermoplastic Columns

et al. 2016

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Phenomena associated with microscale electrophoresis separations cannot, in many cases, be applied to the nanoscale. Thus, understanding the electrophoretic characteristics associated with the nanoscale will help formulate relevant strategies that can optimize the performance of separations carried out on columns with at least one dimension below 150 nm. Electric double layer (EDL) overlap, diffusion, and adsorption/desorption properties and/or dielectrophoretic effects giving rise to stick/slip motion are some of the processes that can play a role in determining the Efficiency of nanoscale electrophoretic separations. We investigated the performance characteristics of electrophoretic separations carried out in nanoslits fabricated in poly(methyl methacrylate), PMMA, devices. Silver nanoparticles (AgNPs) were used as the model system with tracking of their transport via dark field microscopy and localized surface plasmon resonance. AgNPs capped with citrate groups and the negatively charged PMMA walls (induced by O2 plasma modification of the nanoslit walls) enabled separations that were not apparent when these particles were electrophoresed in microscale columns. The separation of AgNPs based on their size without the need for buffer additives using PMMA nanoslit devices is demonstrated herein. Operational parameters such as the electric field strength, nanoslit dimensions, and buffer composition were evaluated as to their effects on the electrophoretic performance, both in terms of Efficiency (plate numbers) and resolution. Electrophoretic separations performed at high electric field strengths (>200 V/cm) resulted in higher plate numbers compared to lower fields due to the absence of stick/slip motion at the higher electric field strengths. Indeed, 60 nm AgNPs could be separated from 100 nm particles in free solution using nanoscale electrophoresis with 100 μm long columns.

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“…It was experimentally and theoretically shown that such interaction can affect the polymer translocation [39, 40, 41]. Such interaction was also investigated using molecular dynamics simulations [42]. Simulation results showed that it is possible, by chemically modifying the pore surface [43], to reduce such interaction and confine DNA near the pore center [42].…”

Section: Discussionmentioning

confidence: 99%

An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation

Luan

Stolovitzky

2013

Nanotechnology

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A solid-state nanopore can be used to sense DNA (or other macromolecules) by monitoring ion-current changes that result from translocation of the molecule through the pore. When transiting a nanopore, the highly negatively charged DNA interacts with a nanopore both electrically and hydrodynamically, causing a current blockage or a current enhancement at different ion concentrations. This effect was previously characterized using a phenomenological model that can be considered as the limit of the electro-hydrodynamics model presented here. We show theoretically that the effect of surface charge of a nanopore (or electroosmotic effect) can be equivalently treated as modifications of electrophoretic mobilities of ions in the pore, providing an improved physical understanding of the current blockage (or enhancement).

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Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer

Cited by 25 publications

References 31 publications

Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels

Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels

Electrophoretic Separation of Single Particles Using Nanoscale Thermoplastic Columns

An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation

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